Genotyping and Genetic Epidemiology. The CIP Genetics Core (CIPGC) has been active in both the generation of genotypic data and in the statistical, bioinformatic and epidemiological analysis of the genetic data. In particular, the work of the Genetics Core over the past year has been used by CIP principal investigators to establish findings for 8 published manuscripts. The CIPGC participated in the study of genetic factors involved in the control of HIV viral load. Manuscripts identified genomic locations in the human genome of major effects in such control. In particular, a region of the 3 untranslated region of the HLA-C gene is targeted by a microRNA resulting in reduced expression of the gene and higher human immunodeficiency virus (HIV) viral loads. We are supporting research investigating the mechanism by which polymorphism in the target site of the microRNA arise and how this affects outcomes in HIV disease. We have been involved in analysis of HLA-C genomic sequences that enabled us to identify the polymorphisms of the binding site and the donor sequence involved in gene conversion at the site, resulting in 2 publications. Additionally we are using bioinformatic analyses to characterize possible roles for this polymorphism of HLA-C and other MHC genes in transplantation outcomes. Following our involvement in implicating polymorphisms in IL28B in HCV clearance in humans, we have characterized the IL28B gene in chimpanzees in order to identify the specific polymorphism directly responsible for HCV clearance. An additional publication involves the characterization of the role of transporter genes in multidrug resistance in cancer stem cells. We are characterizing the sequence and recombinational characteristics as well as integration sites of mouse retroviruses that are derived from endogenous sequences and associated with the generation of thymic lymphoma and initiating work into the role of the microbiome in control of inflammation in this system.